Visible crew/equipment: After Chiana is hurt John goes after Durka in the hangar bay. When Durka fires at John he leaps to take cover, we can see the blue crash mat that John lands on.
Visible crew/equipment: After John rolls the bomb and it explodes under the Nebari ship that Durka's on, when Zhaan shouts at Pilot, "Close the doors!" we can see the puppeteer rod under Pilot's arm as he's trying to shut the doors.
Visible crew/equipment: After the explosion Aeryn shouts for D'Argo to meet her in the maintenance bay, and two shots later while Rygel is on his hoverchair, we can see behind him the equipment/crew member pushing him forward.
Chosen answer: It's never explained. John mentions a theory that his less technologically developed craft simply interferes with the wormhole less than the "superior" Vipers, but they never make a concrete determination on that point. But we also have to take into account the fact that Moya traverses wormholes with no ill effect as well.
Garlonuss ★